Phylodynamic approaches to studying avian influenza virus.

Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.

H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks.

Avian influenza virus subtype H9N2 is endemic in Bangladesh's poultry population. The subtype affects poultry production and poses a potential zoonotic risk. Insufficient understanding of how the poultry trading network shapes the dissemination of avian influenza viruses has hindered the design of targeted interventions to reduce their spread. Here, we use phylodynamic analyses of haemagglutinin sequences to investigate the spatial spread and dispersal patterns of H9N2 viruses in Bangladesh's poultry population, focusing on its two largest cities (Dhaka and Chattogram) and their poultry production and distribution networks. Our analyses suggest that H9N2 subtype avian influenza virus lineage movement occurs relatively less frequently between Bangladesh's two largest cities than within each city. H9N2 viruses detected in single markets are often more closely related to viruses from other markets in the same city than to each other, consistent with close epidemiological connectivity between markets. Our analyses also suggest that H9N2 viruses may spread more frequently between chickens of the three most commonly sold types (sunali-a cross-bred of Fayoumi hen and Rhode Island Red cock, deshi-local indigenous, and exotic broiler) in Dhaka than in Chattogram. Overall, this study improves our understanding of how Bangladesh's poultry trading system impacts avian influenza virus spread and should contribute to the design of tailored surveillance that accommodates local heterogeneity in virus dispersal patterns.

Genomic and epidemiological monitoring of yellow fever virus transmission potential.

The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.

Establishment and cryptic transmission of Zika virus in Brazil and the Americas.

Transmission of Zika virus (ZIKV) in the Americas was first confirmed in May 2015 in northeast Brazil. Brazil has had the highest number of reported ZIKV cases worldwide (more than 200,000 by 24 December 2016) and the most cases associated with microcephaly and other birth defects (2,366 confirmed by 31 December 2016). Since the initial detection of ZIKV in Brazil, more than 45 countries in the Americas have reported local ZIKV transmission, with 24 of these reporting severe ZIKV-associated disease. However, the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of this information for interpreting observed trends in reported microcephaly. Here we address this issue by generating 54 complete or partial ZIKV genomes, mostly from Brazil, and reporting data generated by a mobile genomics laboratory that travelled across northeast Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Analyses of viral genomes with ecological and epidemiological data yield an estimate that ZIKV was present in northeast Brazil by February 2014 and is likely to have disseminated from there, nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates for the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. The role of northeast Brazil in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the basic reproduction number of the virus.

Zika vírus in the americas: early epidemiological and genetic findings

Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015, and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. We performed next-generation sequencing to generate seven Brazilian ZIKV genomes sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Results of phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, which we estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV-endemic areas, as well as with reported outbreaks in the Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however...(AU)

Bacille Calmette-Guerin disease following Bacille Calmette-Guerin vaccination of an HIV-infected health-care worker.

We present a case of Bacille Calmette-Guerin (BCG) lymphadenitis following immunization of a health-care worker with risk factors for HIV but undiagnosed infection. This case highlights the potential risks of BCG and clearly demonstrates the need to consider HIV testing in all patients prior to BCG vaccination.

Sexual health of transgender sex workers attending an inner-city genitourinary medicine clinic.

Previous studies have reported high HIV prevalence among transgender sex workers (TSWs). We performed a retrospective case-note review of known TSWs attending our unit. In all, 16/24 (66.7%) of patients were diagnosed with at least one sexually transmitted infection (STI) and 7/24 (29.2%) reported intentional unprotected anal or vaginal intercourse, which may explain the high prevalence of HIV in our cohort (37.5%). TSWs disclosed high rates of substance misuse, violence and sexual assault, which may also contribute to the increased prevalence of STI in this group.

Is screening for pharyngeal Chlamydia trachomatis warranted in high-risk groups?

A recent survey reported that 36% of UK genitourinary medicine clinics offer testing for pharyngeal Chlamydia trachomatis (CT). Screening at this site is targeted at high-risk groups attending our centre, including female sex workers (FSWs) and male sex workers (MSWs). A total of 2406 patients were screened between November 2006 and October 2007. A retrospective case-note review was performed for positive cases. The prevalence of pharyngeal CT was 1.9% in both men and women. The mean number of sexual partners reported in the preceding three months was 168 and 56 for FSWs and MSWs, respectively. Lack of consistent condom use and high numbers of sexual partners identify this population as potential core transmitters of infection. While the British Association of Sexual Health and HIV (BASHH) guidelines do not recommend routine screening for pharyngeal CT, there may be a role in selected high-risk populations.

An audit on the management of lymphogranuloma venereum in a sexual health clinic in London, UK.

We performed an audit on the management of lymphogranuloma venereum (LGV) against the British Association of Sexual Health and HIV (BASHH) guidelines. Sixty-three cases of LGV were diagnosed in 60 men who have sex with men (MSM). Fifty-six out of 63 (89%) episodes were treated in accordance with the guidelines. Although all eligible patients were offered an HIV test, 10% and 29% of patients were not offered syphilis or hepatitis C tests, respectively, at the time of LGV diagnosis. Partner notification was not possible in a third of cases. Several patients were re-infected with rectal Chlamydia trachomatis in the three months following LGV diagnosis, emphasizing the importance of rescreening to detect new infections as well as treatment failures in MSM at ongoing high risk of sexually transmitted infection acquisition.

Smoking in the home and children's health.

OBJECTIVES: We estimate for young children the annual excess health service use, healthcare expenditures, and disability bed days for respiratory conditions associated with exposure to smoking in the home in the United States. METHODS: Health service use, healthcare expenditures and disability bed days data come from the 1999 and 2001 Medical Expenditure Panel Survey (MEPS). Reported smoking in the home comes from the linked National Health Interview Survey, from which the MEPS sample is drawn. Multivariate statistical analysis controls for potential confounding factors. The sample is 2759 children aged 0-4. RESULTS: Smoking in the home is associated with an increase in the probability of emergency department visits for respiratory conditions by five percentage points and the probability of inpatient use for these conditions by three percentage points. There is no relation between indoor smoking by adults and either ambulatory visits or prescription drug expenditures. Overall, indoor smoking is associated with $117 in additional healthcare expenditures for respiratory conditions for each exposed child aged 0-4. Indoor smoking is also associated with an eight percentage point increase in the probability of having a bed day because of respiratory illness for children aged 1-4. CONCLUSIONS: Despite the significant progress made in tobacco control, many children are still exposed to secondhand smoke in their home. Reducing exposure to smoking in the home would probably reduce healthcare expenditures for respiratory conditions and improve children's health.

The relation between skeletal maturation and adiposity in African American and Caucasian children.

OBJECTIVE: African American children have earlier pubertal and skeletal maturation and a higher body mass index (BMI) than Caucasian children. We tested the hypothesis that advanced bone age in African American children is accounted for by their greater adiposity. STUDY DESIGN: We studied 252 African American (n = 97) and Caucasian (n = 155) children aged 5 to 12 years. Skeletal age was determined by a radiologist blinded to clinical details. The difference between bone age (BA) and chronological age (CA) (noted as BA - CA) and the ratio of bone age to chronological age (BA/CA) were determined. Analysis of covariance was used to adjust skeletal maturation for the effects of adiposity, as measured by BMI, BMI standard deviation score (BMI SDS), and fat mass by dual energy x-ray absorptiometry (DXA). RESULTS: African American children were significantly heavier than Caucasians (BMI SDS 2.7 +/- 3.4 vs 1.7 +/- 2.4, P <.05). Both BA - CA (0.75 +/- 1.46 vs 0.28 +/- 1.38, P <.05) and BA/CA (1.09 +/- 0.17 vs 1.03 +/- 0.16, P <.05) were significantly greater in African Americans than Caucasians. BA - CA and BA/CA were significantly correlated with lean body mass, BMI, BMI SDS, and DXA fat mass (all r > 0.46, P <.001). Neither BA - CA nor BA/CA of African Americans and Caucasians were significantly different after correction for lean body mass and measures of adiposity, including BMI, BMI SDS, or DXA fat mass. CONCLUSION: Skeletal age is more advanced in African American than Caucasian children and is significantly related to body mass. In large measure, the advancement in skeletal maturation of prepubertal and early pubertal African American children can be accounted for by their greater adiposity.

Direct evidence that leukemic cells present HLA-associated immunogenic peptides derived from the BCR-ABL b3a2 fusion protein.

The BCR-ABL oncogene is central in the pathogenesis of chronic myeloid leukemia (CML). Here, tandem nanospray mass spectrometry was used to demonstrate cell surface HLA-associated expression of the BCR-ABL peptide KQSSKALQR on class I-negative CML cells transfected with HLA-A*0301, and on primary CML cells from HLA-A3-positive patients. These patients mounted a cytotoxic T-lymphocyte response to KQSSKALQR that also killed autologous CML cells, and tetramer staining demonstrated the presence of circulating KQSSKALQR-specific T cells. The findings are the first demonstration that CML cells express HLA-associated leukemia-specific immunogenic peptides and provide a sound basis for immunization studies against BCR-ABL.

Glucocorticoid excess during adolescence leads to a major persistent deficit in bone mass and an increase in central body fat.

Endogenous Cushing's syndrome (CS) in children causes growth retardation, decreased bone mass, and increased total body fat. No prospective controlled studies have been performed in children to determine the long-term sequelae of CS on peak bone mass and body composition. A 15-year-old girl with Cushing disease (CD), and her healthy identical co-twin, were followed for 6 years after the CD was cured. At the 6-year follow-up both twins had areal bone mineral density (BMD) and body composition determined by dual-energy X-ray absorptiometry (DXA) and three-dimensional quantitative computed tomography (3DQCT). Z scores for height, weight, and body mass index (BMI) were -2.3, -0.8 and 0.2, and 1.2, 0.2, and -0.6, in the twin with CD and her co-twin, respectively. In the twin with CD, areal BMD and bone mineral apparent density (BMAD) at different sites varied from 0.7 to 3 SD below her co-twin. Volumetric lumbar spine bone density Z score was -0.75 and 1.0, and total body, abdominal visceral, and subcutaneous fat (%) was 42, 10, and 41 versus 26, 4, and 17 in the twin with CD and her co-twin, respectively. The relationship between total body fat and L2-L4 BMAD was inverse in the twin with CD (p < 0.05), which by contrast in her co-twin was opposite and direct (p < 0.001). In the twin with CD, despite cure, there was a persistent deficit in bone mass and increase in total and visceral body fat. These observations suggest that hypercortisolism (exogenous or endogenous) during adolescence may have persistent adverse effects on bone and fat mass.

Fluorescence from airborne microparticles: dependence on size, concentration of fluorophores, and illumination intensity.

We measured fluorescence from spherical water droplets containing tryptophan and from aggregates of bacterial cells and compared these measurements with calculations of fluorescence of dielectric spheres. The measured dependence of fluorescence on size, from both droplets and dry-particle aggregates of bacteria, is proportional to the absorption cross section calculated for homogeneous spheres containing the appropriate percentage of tryptophan. However, as the tryptophan concentration of the water droplets is increased, the measured fluorescence from droplets increases less than predicted, probably because of concentration quenching. We model the dependence of the fluorescence on input intensity by assuming that the average time between fluorescence emission events is the sum of the fluorescence lifetime and the excitation lifetime (the average time it takes for an illuminated molecule to be excited), which we calculated assuming that the intensity inside the particle is uniform. Even though the intensity inside the particles spatially varies, this assumption of uniform intensity still leads to results consistent with the measured intensity dependence.

Scattering and Internal Fields of a Microsphere that Contains a Saturable Absorber: Finite-Difference Time-Domain Simulations.

Illumination intensities that are used to induce scattering and fluorescence in aerosols can be large enough to cause variations in the refractive index. Methods used to calculate the scattering from homogeneous particles may not be valid for these systems. We use the finite-difference time-domain method and an iterative technique to model scattering by microspheres that contain a saturable absorber. We illustrate this technique by calculating the scattering from spheres that contain tryptophan. We show the Mueller scattering matrices along with the internal intensity distributions for different incident intensities. The backscattering increases as the illumination intensity becomes large enough to saturate the absorption in regions of the sphere.

Sclerosing bone dysplasias: genetic and radioclinical features.

Although knowledge of basic genetics in the field of sclerosing bone dysplasias is progressing, the radiologist still plays a pivotal role in the diagnosis of this relatively poorly understood group of disorders. Based on a target site approach, these anomalies are classified into three groups. Within each group, further differentiation can be made by distinctive clinical findings and by mode of inheritance: (a) dysplasias of endochondral bone formation: osteopetrosis (Albers-Schönberg disease), pycnodysostosis, enostosis, osteopoikilosis, osteopathia striata (Voorhoeve disease); (b) dysplasias of intramembranous bone formation: progressive diaphyseal dysplasia (Camurati-Engelmann disease) and variants, hyperostosis corticalis generalisata (Van Buchem disease) and variants; and (c) mixed sclerosing dysplasias: melorheostosis (Leri disease) and overlap syndromes.